MAST - Motif Alignment and Search Tool
MAST version 3.0 (Release date: 2001/03/01 11:41:04)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.sdsc.edu.
REFERENCE
If you use this program in your research, please cite:
Timothy L. Bailey and Michael Gribskov,
"Combining evidence using p-values: application to sequence homology
searches", Bioinformatics, 14(48-54), 1998.
DATABASE AND MOTIFS
DATABASE farntrans5.s (peptide)
Last updated on Thu Mar 1 08:28:38 2001
Database contains 5 sequences, 1900 residues
MOTIFS meme.farntrans5.tcm.4.sunsparcsolaris.html (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 30 GGFQGRPNKEVHTCYTYWALAALAILNKLH
2 14 INKEKLIQWIKSCQ
3 10 GWWLCERQLP
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1 2
----- ----- -----
2 0.22
3 0.19 0.18
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058
L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064
W 0.013 Y 0.033
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 5 sequences has E-value less than 10.
- The E-value of a sequence is the expected number of sequences
in a random database of the same size that would match the motifs as
well as the sequence does and is equal to the combined p-value of the
sequence times the number of sequences in the database.
- The combined p-value of a sequence measures the strength of the
match of the sequence to all the motifs and is calculated by
- finding the score of the single best match of each motif
to the sequence (best matches may overlap),
- calculating the sequence p-value of each score,
- forming the product of the p-values,
- taking the p-value of the product.
- The sequence p-value of a score is defined as the
probability of a random sequence of the same length containing
some match with as good or better a score.
- The score for the match of a position in a sequence to a motif
is computed by by summing the appropriate entry from each column of
the position-dependent scoring matrix that represents the motif.
- Sequences shorter than one or more of the motifs are skipped.
- The table is sorted by increasing E-value.
| Links | Sequence Name | Description | E-value | Length
|
|---|
|
| BET2_YEAST
| YPT1/SEC4 PROTEINS GERANY...
| 7.4e-37
| 325
|
|
| RATRABGERB
| Rat rab geranylgeranyl tr...
| 3.6e-35
| 331
|
|
| CAL1_YEAST
| RAS PROTEINS GERANYLGERAN...
| 2.6e-21
| 376
|
|
| PFTB_RAT
| PROTEIN FARNESYLTRANSFERA...
| 4.4e-20
| 437
|
|
| RAM1_YEAST
| PROTEIN FARNESYLTRANSFERA...
| 5.1e-19
| 431
|
SECTION II: MOTIF DIAGRAMS
- The ordering and spacing of all non-overlapping motif occurrences
are shown for each high-scoring sequence listed in Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001.
- The POSITION p-value of a match is the probability of
a single random subsequence of the length of the motif
scoring at least as well as the observed match.
- For each sequence, all motif occurrences are shown unless there
are overlaps. In that case, a motif occurrence is shown only if its
p-value is less than the product of the p-values of the other
(lower-numbered) motif occurrences that it overlaps.
- The table also shows the E-value of each sequence.
- Spacers and motif occurences are indicated by
- occurrence of motif `n' with p-value less than 0.0001.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
| Links | Name | Expect |    Motifs
|
|---|
|
| BET2_YEAST
| 7.4e-37
|
|
|
| RATRABGERB
| 3.6e-35
|
|
|
| CAL1_YEAST
| 2.6e-21
|
|
|
| PFTB_RAT
| 4.4e-20
|
|
|
| RAM1_YEAST
| 5.1e-19
|
|
| SCALE
|
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| 1
| 25
| 50
| 75
| 100
| 125
| 150
| 175
| 200
| 225
| 250
| 275
| 300
| 325
| 350
| 375
| 400
| 425
| 450
| |
|
|---|
SECTION III: ANNOTATED SEQUENCES
- The positions and p-values of the non-overlapping motif occurrences
are shown above the actual sequence for each of the high-scoring
sequences from Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001 as
defined in Section II.
- For each sequence, the first line specifies the name of the sequence.
- The second (and possibly more) lines give a description of the
sequence.
- Following the description line(s) is a line giving the length,
combined p-value, and E-value of the sequence as defined in Section I.
- The next line reproduces the motif diagram from Section II.
- The entire sequence is printed on the following lines.
- Motif occurrences are indicated directly above their positions in the
sequence on lines showing
- the motif number of the occurrence,
- the position p-value of the occurrence,
- the best possible match to the motif, and
- columns whose match to the motif has a positive score (indicated
by a plus sign).
BET2_YEAST
YPT1/SEC4 PROTEINS GERANYLGERANYLTRANSFERASE BETA SUBUNIT (EC 2.
LENGTH = 325 COMBINED P-VALUE = 1.48e-37 E-VALUE = 7.4e-37
DIAGRAM: 6-[2]-3-[1]-1-[2]-4-[1]-4-[2]-3-[1]-1-[2]-3-[1]-10-[3]-1-[1]-1- [2]-4-[1]-24
[2] [1] [2] [1]
5.2e-05 2.7e-10 6.6e-10 5.9
INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGF
+++ +++++++ ++ + +++ +++ +++++ +++++++ + ++++++++++++++ + +
1 MSGSLTLLKEKHIRYIESLDTNKHNFEYWLTEHLRLNGIYWGLTALCVLDSPETFVKEEVISFVLSCWDDKYGAF
[2] [1]
e-14 4.8e-07 2.3e-17
QGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILN
+ +++++++ + ++++++ +++++ +++ +++++++ ++ + ++++ +++++++ +++++++++++
76 APFPRHDAHLLTTLSAVQILATYDALDVLGKDRKVRLISFIRGNQLEDGSFQGDRFGEVDTRFVYTALSALSILG
[2] [1] [3] [1]
5.1e-07 1.4e-18 1.2e-14 4.6
KLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH GWWLCERQLP GGF
+++ ++++ ++++++++ ++++ ++++++++++++++++++++++++ ++++++++++ +++
151 ELTSEVVDPAVDFVLKCYNFDGGFGLCPNAESHAAQAFTCLGALAIANKLDMLSDDQLEEIGWWLCERQLPEGGL
[2] [1]
e-22 2.0e-13 3.8e-17
QGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKL
++++ ++++++++++++++++++++++ ++ +++++++++++ ++++++++++++++++ ++++++++++ +
226 NGRPSKLPDVCYSWWVLSSLAIIGRLDWINYEKLTEFILKCQDEKKGGISDRPENEVDVFHTVFGVAGLSLMGYD
H
+
301 NLVPIDPIYCMPKSVTSKFKKYPYK
RATRABGERB
Rat rab geranylgeranyl transferase beta-subunit
LENGTH = 331 COMBINED P-VALUE = 7.22e-36 E-VALUE = 3.6e-35
DIAGRAM: 65-[2]-3-[1]-1-[2]-3-[1]-1-[2]-3-[1]-7-[3]-1-[1]-1-[2]-4-[1]-26
[2]
1.0e-11
INKEKLIQWI
+++++++ ++
1 MGTQQKDVTIKSDAPDTLLLEKHADYIASYGSKKDDYEYCMSEYLRMSGVYWGLTVMDLMGQLHRMNKEEILVFI
[1] [2] [1]
1.6e-14 1.4e-09 5.4e-19
KSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWAL
++++ ++ + +++++++ ++ ++++++++++++ +++++++ ++++++ + ++++++++++++++++++
76 KSCQHECGGVSASIGHDPHLLYTLSAVQILTLYDSIHVINVDKVVAYVQSLQKEDGSFAGDIWGEIDTRFSFCAV
[2] [1] [3]
3.8e-12 4.8e-19 1.2e-14
AALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH GWWLCERQLP
++++++++++ ++++++++++++++ ++++++++ ++++++++++++ ++++++++ ++++++++++
151 ATLALLGKLDAINVEKAIEFVLSCMNFDGGFGCRPGSESHAGQIYCCTGFLAITSQLHQVNSDLLGWWLCERQLP
[1] [2] [1]
3.9e-21 1.2e-12 9.6e-18
GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAI
+++++++++++++++++++++++ ++++++ ++++++++++++++ ++++++++++++ +++ ++++++++
226 SGGLNGRPEKLPDVCYSWWVLASLKIIGRLHWIDREKLRSFILACQDEETGGFADRPGDMVDPFHTLFGIAGLSL
LNKLH
+++++
301 LGEEQIKPVSPVFCMPEEVLQRVNVQPELVS
CAL1_YEAST
RAS PROTEINS GERANYLGERANYLTRANSFERASE (EC 2.5.1.-) (PROTEIN GER
LENGTH = 376 COMBINED P-VALUE = 5.22e-22 E-VALUE = 2.6e-21
DIAGRAM: 125-[2]-50-[2]-1-[1]-4-[2]-22-[1]-22-[1]-5-[2]-1
[2]
1.8e-08
INKEKLIQWIKSCQ
+++++++++++++
76 LDDTENTVISGFVGSLVMNIPHATTINLPNTLFALLSMIMLRDYEYFETILDKRSLARFVSKCQRPDRGSFVSCL
[2] [1]
4.8e-10 8.7e-14
INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALA
+++++++ ++++++ + + + +++++ +++ ++++
151 DYKTNCGSSVDSDDLRFCYIAVAILYICGCRSKEDFDEYIDTEKLLGYIMSQQCYNGAFGAHNEPHSGYTSCALS
[2] [1]
5.9e-08 5.9e-20
ALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAIL
+++++++++ ++++++++++++ +++++++++ +++++++++++++ ++
226 TLALLSSLEKLSDKFKEDTITWLLHRQVSSHGCMKFESELNASYDQSDDGGFQGRENKFADTCYAFWCLNSLHLL
[1] [2]
4.0e-13 2.1e-07
NKLH GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ
++++ ++++ + ++++++++++ + +++++++ + ++ +++++++++
301 TKDWKMLCQTELVTNYLLDRTQKTLTGGFSKNDEEDADLYHSCLGSAALALIEGKFNGELCIPQEIFNDFSKRCC
PFTB_RAT
PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARNES
LENGTH = 437 COMBINED P-VALUE = 8.75e-21 E-VALUE = 4.4e-20
DIAGRAM: 120-[2]-3-[1]-4-[2]-3-[1]-1-[2]-3-[1]-1-[2]-4-[1]-14-[2]-4-[1]-60
[2] [1]
1.3e-07 2.8e-19
INKEKLIQWIKSCQ GGFQGRPNKEVHT
++ ++++++++ ++ +++++++++ +++
76 EKHFHYLKRGLRQLTDAYECLDASRPWLCYWILHSLELLDEPIPQIVATDVCQFLELCQSPDGGFGGGPGQYPHL
[2] [1] [2]
2.3e-09 2.1e-14 1.8e-0
CYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKL
+ +++++++++++++++ ++++++++++ +++ + + ++ +++++++ +++++++++++++++ + +++
151 APTYAAVNALCIIGTEEAYNVINREKLLQYLYSLKQPDGSFLMHVGGEVDVRSAYCAASVASLTNIITPDLFEGT
[1] [2] [1]
8 7.4e-20 1.8e-08 2.2e-16
IQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCY
++++ +++ +++++ +++++++++++++++++ ++++++ + +++++++++++ ++++++ ++++++++
226 AEWIARCQNWEGGIGGVPGMEAHGGYTFCGLAALVILKKERSLNLKSLLQWVTSRQMRFEGGFQGRCNKLVDGCY
[2] [1]
5.0e-08 3.1e-15
TYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNK
++++++ + ++++ ++++++++++++++ +++ +++++ +++++++++++++++++
301 SFWQAGLLPLLHRALHAQGDPALSMSHWMFHQQALQEYILMCCQCPAGGLLDKPGKSRDFYHTCYCLSGLSIAQH
LH
+
376 FGSGAMLHDVVMGVPENVLQPTHPVYNIGPDKVIQATTHFLQKPVPGFEECEDAVTSDPATD
RAM1_YEAST
PROTEIN FARNESYLTRANSFERASE BETA SUBUNIT (EC 2.5.1.-) (CAAX FARN
LENGTH = 431 COMBINED P-VALUE = 1.01e-19 E-VALUE = 5.1e-19
DIAGRAM: 144-[1]-5-[2]-4-[1]-1-[2]-4-[1]-1-[2]-4-[1]-4-[2]-5-[1]-35-[2]-4
[1]
8.8e-1
GGFQGR
+ ++++
76 PALTKEFHKMYLDVAFEISLPPQMTALDASQPWMLYWIANSLKVMDRDWLSDDTKRKIVVKLFTISPSGGPFGGG
[2] [1]
7 6.4e-07 1.0e-13
PNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNK
++++++++ ++++++++++ ++++ ++++++++++ +++ + ++ ++++++++ +++++++++++++
151 PGQLSHLASTYAAINALSLCDNIDGCWDRIDRKGIYQWLISLKEPNGGFKTCLEVGEVDTRGIYCALSIATLLNI
[2] [1] [2] [1]
2.5e-08 3.1e-17 4.7e-11 2.4e-
LH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQG
++ + ++++++++++++ + ++ +++++++++++++++++++++++ ++++++++++++++ ++ +
226 LTEELTEGVLNYLKNCQNYEGGFGSCPHVDEAHGGYTFCATASLAILRSMDQINVEKLLEWSSARQLQEERGFCG
[2] [1]
16 4.9e-09 2.7e-13
RPNKEVHTCYTYWALAALAILNKLH INKEKLIQWIKSCQ GGFQGRPNKEVHTCYTYWALAALAILN
+ ++++++++++++ +++++++++ +++++++++++ ++ +++++++++++++++ +++ ++++++
301 RSNKLVDGCYSFWVGGSAAILEAFGYGQCFNKHALRDYILYCCQEKEQPGLRDKPGAHSDFYHTNYCLLGLAVAE
[2]
9.8e-05
KLH INKEKLIQWIKSCQ
+ +++++++ + +++
376 SSYSCTPNDSPHNIKCTPDRLIGSSKLTDVNPVYGLPIENVRKIIHYFKSNLSSPS
Debugging Information
CPU: nbcr2
Time 0.230000 secs.
mast meme.farntrans5.tcm.4.sunsparcsolaris.html -stdout
Button Help
Links to Entrez database at NCBI
Links to sequence scores (section I)
Links to motif diagrams (section II)
Links to sequence/motif annotated alignments (section III)
This information